Analytical Validation of a Novel 6-Gene Signature for Prediction of Distant Recurrence in Estrogen Receptor-Positive, HER2-Negative, Early-Stage Breast Cancer.

Abstract

BACKGROUND:

OncoMasTR is a recently developed multigene prognostic test for early-stage breast cancer. The test has been developed in a kit-based format for decentralized deployment in molecular pathology laboratories. The analytical performance characteristics of the OncoMasTR test are described in this study.

METHODS:

Expression levels of 6 genes were measured by 1-step reverse transcription-quantitative PCR on RNA samples prepared from formalin-fixed, paraffin-embedded (FFPE) breast tumor specimens. Assay precision, reproducibility, input range, and interference were determined using FFPE-derived RNA samples representative of low and high prognostic risk scores. A pooled RNA sample derived from 6 FFPE breast tumor specimens was used to establish the linear range, limit of detection, and amplification efficiency of the individual gene expression assays.

RESULTS:

The overall precision of the OncoMasTR test was high with an SD of 0.16, which represents less than 2% of the 10-unit risk score range. Test results were reproducible across 4 testing sites, with correlation coefficients of 0.94 to 0.96 for the continuous risk score and concordance of 86% to 96% in low-/high-risk sample classification. Consistent risk scores were obtained across a > 100-fold RNA input range. Individual gene expression assays were linear up to quantification cycle values of 36.0 to 36.9, with amplification efficiencies of 80% to 102%. Test results were not influenced by agents used during RNA isolation, by low levels of copurified genomic DNA, or by moderate levels of copurified adjacent nontumor tissue.

CONCLUSION:

The OncoMasTR prognostic test displays robust analytical performance that is suitable for deployment by local pathology laboratories for decentralized use.

• Authors: Tony Loughman, Stephen Barron, Chan-Ju Angel Wang, Peter Dynoodt, Bozena Fender, Cesar Lopez-Ruiz, Sharon Stapleton, Aurelie Fabre, Cecily Quinn, Bjorn Nodin, Karin Jirström, Fatemeh Razmara, Anthony O'Grady, Anne-Marie Baird, Steven G Gray, Ana Freixo, Cathy B Moelans, Paul J van Diest, Michael J Duffy, Desmond O'Leary, John Crown, Adrian P Bracken, William M Gallagher
• Journal: Clinical chemistry (Clin Chem) Vol. 68 Issue 6 Pg. 837-847 (06 01 2022) ISSN: 1530-8561 [Electronic] England
• PMID: 35312747 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © American Association for Clinical Chemistry 2022.

Chemical References

• Biomarkers, Tumor
• Receptors, Estrogen
• Formaldehyde
• RNA

Topics

• Biomarkers, Tumor (genetics)
• Breast (pathology)
• Breast Neoplasms (pathology)
• Female
• Formaldehyde
• Gene Expression Profiling (methods)
• Humans
• Paraffin Embedding
• Prognosis
• RNA (analysis)
• Receptors, Estrogen (metabolism)
• Reproducibility of Results